Data on genomic profiles, epigenomic profiles, phenotypic and functional characteristics of primary human Langerhans cells

In this study, the authors analysed primary human Langerhans cells (LCs), using bulk and single-cell RNAseq as well as H3K4Me3 and H4K27Ac chromatin immunoprecipitation sequencing (ChIPseq), and coupled these genomic and epigenomic profiles with LC phenotypic and functional characteristics.

Data access: RNA-seq, scRNA-seq and ChiP-seq data generated during the current study, are publicly available in the NCBI Gene Expression Omnibus repository at: https://identifiers.org/geo:GSE120386. Data supporting figures 1-6 and supplementary figures 1-4 are publicly available in the figshare repository at: https://doi.org/10.6084/m9.figshare.11372013.

Dataset description:
This data record consists of one data set, Source_data.xlsx, in .xlsx file format. The dataset contains a total of 19 sheets labelled Figure 1d, Figure 1e, Figure 2a, Figure 2c, Figure 2d, Figure 2e, Figure 3c, Figure 4a, Figure 4d, Figure 5b, Figure 5c, Figure 6b, Figure 6d, Sup Fig 1c, Sup Fig 2b, Sup Fig 2d, Sup Fig 2f, Sup Fig 4a and Sup Fig 4d.

Sheet “Figure 1d” contains the raw data used to generate figure 1d. Data contain interferon gamma (IFN-γ) secretion levels of steady-state and migrated LCs, that were either pulsed (with 30 amino acid peptide containing the Epstein-Barr virus (EBV) epitope) or unpulsed.

Sheet “Figure 1e” contains the raw data used to generate figure 1e. Data contain IFN-γ secretion by EBV-specific CD8 T cell line stimulated by pulsed migrated LCs. IFN-γ secretion was measured with or without (Medium) TNF stimulation.

Sheet “Figure 2a” contains the raw data used to generate figure 2a. Data contain the results of Gene ontology analysis for each expression level interval determined by RNA-seq. Analysis was performed using ToppGene on-line tool.

Sheet “Figure 2c” contains the raw data used to generate figure 2c. Data contain the intracellular expression of SQSTM1 and TRIM21 measured by flow cytometry in steady-state and migrated LCs.

Sheet “Figure 2d” contains the raw data used to generate figure 2d. Data contain the gene expression levels of 13 genes in tumor necrosis factor (TNF)-stimulated (T24) LCs. Expression levels of 3 biological replicates for each gene are shown.

Sheet “Figure 2e” contains the raw data used to generate figure 2e. Data contain the gene expression levels of 10 genes in LCs stimulated with TNF for 24 hours (T24), for 2 hours (T2) and 0 hours (T0). Expression levels of 3 biological replicates for each gene are shown.

Sheet “Figure 3c” contains the raw data used to generate figure 3c. Data contain the results of Gene ontology analysis for marker genes (n=100) representative of indicated cluster, performed using ToppGene. –log(10) Benjamini Hochberg corrected p values are shown for cluster-specific processes.

Sheet “Figure 4a” contains the raw data used to generate figure 4a. Data contain the number of differentially expressed genes (DEGs) and the number of DEGs with the H3K27Ac mark in LCs following stimulation with TNF. Results are shown for genes upregulated early (2h), and for genes upregulated late (24h).

Sheet “Figure 4d” contains the raw data used to generate figure 4d. Transcripts with the H3K4Me3 and H3K27Ac marks were identified. This sheet shows the biological processes enriched in those genes, detected using ToppGene based on false discover rate (FDR) corrected p-values for gene Ontology (GO) categories.

Sheet “Figure 5b” contains the raw data used to generate figure 5b. Data show the IRF4 protein expression (expressed as %) in steady state vs migrated LCs. IRF4+ LCs (%) was measured by flow cytometry.

Sheet “Figure 5c” contains the raw data used to generate figure 5c. Data show the expression levels of the key transcription factors in migrated LCs before (0h), and after TNF stimulation (2h, 24h). Results of three biological donors are shown.

Sheet “Figure 6b” contains the raw data used to generate figure 6b. Data show Mean fluorescence intensity (MFI) of IRF4 expressing CD207+ CD1a+ live LCs (in CRISPR-Cas9 edited (KD) and control (WT) migrated LCs).

Sheet “Figure 6d” contains the raw data used to generate figure 6d. Data show the results of the GO processes and pathways differentially enriched in control LC (WT) versus IRF4 CRISPR-Cas9 edited LCs (IRF4 KD).

Sheet “Sup Fig 1c” contains the raw data used to generate supplementary figure 1c. Data show IFN-γ secretion levels of pulsed (with 9 amino acid peptide GLC) or unpulsed LCs that were stimulated with TNF.

Sheet “Sup Fig 2b” contains the raw data used to generate supplementary figure 2b. Data show log(2) FPKM gene expression levels for genes involved in antigen processing and presentation in LCs. Results of three biological donors are shown (LC1, LC2, LC3).

Sheet “Sup Fig 2e” contains the raw data used to generate supplementary figure 2e.
Data show gene expression of PSME2 and CAV1 in migrated LC assessed by qPCR before (medium) and following stimulation with TNF.

Sheet “Sup Fig 2f” contains the raw data used to generate supplementary figure 2f. Data show Log (2) Fragments Per Kilobase of transcript per Million mapped reads (FPKM) median expression values for each gene included in the antigen presentation class I signature from Reactome database. Expression levels of each gene are shown before (T0) and after (T2, T24) stimulation with TNF.

Sheet “Sup Fig 4a” contains the raw data used to generate supplementary figure 4a. Data show the number of DAGs and the number of DAGs with the H3K27Ac mark at 2h and 24h in clusters of coexpressed genes up-regulated early (2h, clusters 3) and late (24h, cluster 2) during
stimulation with TNF.

Sheet “Sup Fig 4d” contains the raw data used to generate supplementary figure 4a. Peaks H3K4Me3 and H3K27Ac T0 datasets were scanned for ISRE/AICE/EICE binding
motifs. 1193 consensus genes (present in all 3 biological replicates with both chromatin marks) were identified. Biological processes enriched in those genes (shown in this sheet) were detected using ToppGene (FDR corrected p-values for GO categories).

Study aims and methodology:
LC are highly specialised antigen presenting cells, priming protective immune responses against pathogens encountered via the skin, such as viruses, bacteria and fungi. The authors used transcriptional and chromatin profiling and showed that migratory LCs are robustly programmed for MHC-I and MHC-II antigen presentation as well as mitochondrial oxidative phosphorylation.
The following methods are described in more detail in the published article: cell isolation (from skin specimens and blood samples of healthy individuals) and stimulation with TNF, antigen cross-presentation assay, flow cytometry, RNA-seq, quantitative reverse transcription polymerase chain reaction (qRT PCR), ChIP-seq, Drop-seq, bioinformatics analysis of sequencing data and CRISPR-Cas9 gene editing.